I look forward to a response, as I asked a similar question when having some issues with my newly installed system a couple of months back, but never really received an answer. For example, how long does an error have to be present before the controller reports it? If a component on the system fails to respond, will evohome retry a few times before throwing an error?
FWIW, my issue was ultimately solved by completely resetting my controller and all HR92s. I probably didn't need to do all the HR92s, but I wasn't going to risk any further problems. However, my comms fault would always appear about 4 hours after restarting the evo controller (with a hammer, as you say!), whereas it sounds like your fault is a little more transient. My signal levels were all perfect, and I even tried deleting the problematic zones and clearing their respective HR92s then re-created them, all to no avail. There really needs to be more information made available about how the evo system works - even the installer training and RF guidelines PDF don't provide anything beyond basic rules about how and where RF devices should be installed.